The 21-year-old, who scored in both of Brazil's friendly victories during the international break, owed much to strike partner Zlatan Ibrahimovic for setting up his efforts.
First Pato expertly volleyed in a delicate Ibrahimovic cross from the left after 18 minutes, sending the ball back across the goalkeeper having patiently waited for it to drop.
Ibrahimovic then took a quick free kick on the half hour with the Chievo defence asleep and Pato blasted home to send a warning to Tuesday's Champions League opponents Real Madrid.
Ibrahimovic was unfortunate to divert a corner into his own net midway through the second half and the visitors were close to snatching a draw before substitute Robinho netted his first Milan goal by rounding the keeper in stoppage-time.
"I'm just doing my job, a job for the team. I'm happy with my two goals," Pato, who has again struggled for fitness this term, told Sky television.
ROMA VICTORY
Ibrahimovic was also carrying a slight groin problem but played the full game to show he is in shape for the Bernabeu.
Brazil defender Thiago Silva, courted by Real in the close season, is doubtful for Tuesday though after being carried off with a painful ankle injury.
Milan's most famous Brazilian, Ronaldinho, again had a quiet game in his new position behind the strikers rather than on the left although he did have two late shots.
In Saturday's other Serie A game, last term's runners-up AS Roma recorded only their second league win of the campaign with a nervous 2-1 victory over Genoa at the Stadio Olimpico.
Former Genoa striker Marco Borriello, who earlier hit the post, opened the scoring when he prodded in Francesco Totti's deflected cross before Matteo Brighi showed bravery to make it 2-0 after the break.
Genoa had a host of chances, including ex-Roma forward Luca Toni heading wide, but they eventually found the net through Gergely Rudolf and kept the pressure on until the end.
